Neighbor Optimization MRE¶
This Jupyter notebook (05.02) details the analysis steps to optimize the nearest neighbor analysis.
THIS ANALYSIS STEP DOES NOT OUTPUT AN H5AD FILE.
Initialize Environment¶
First import all the necessary packages here:
InĀ [1]:
# Import necessary packages
import os
import scanpy as sc
import numpy as np
import pandas as pd
import anndata as ad
from datetime import datetime as dt
# Scanpy settings
sc.settings.verbosity = 3
sc.logging.print_header()
# Set working directory
os.chdir("/home/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization")
adata = "01_25-12-05-17-25_preprocessing_MRE.h5ad"
2025-12-05 22:27:57.336510: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
scanpy==1.9.5 anndata==0.10.2 umap==0.5.4 numpy==1.24.4 scipy==1.11.3 pandas==2.1.1 scikit-learn==1.3.1 statsmodels==0.14.0 igraph==0.11.2 louvain==0.8.1 pynndescent==0.5.10
Identify the starting directory. Get a timestamp for the run.
InĀ [2]:
# Determine work location
print("The work location for this notebook is: " + os.getcwd() + "\n")
# Get a timestamp for the start of the run
timestamp = dt.now()
print("This notebook was last run on " + timestamp.strftime("%y-%m-%d %H:%M") + "\n")
The work location for this notebook is: /blue/m.pipkin/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization This notebook was last run on 25-12-05 22:28
The work directory is structured to contain a folder named "h5ad" which itself contains output from previous analysis steps. Import data from the latest analysis:
InĀ [3]:
# List items in outs folder
adata = ad.read_h5ad("../../h5ad/" + adata)
# Inspect AnnData
print(adata)
AnnData object with n_obs Ć n_vars = 28407 Ć 18505
obs: 'experiment', 'group', 'timepoint', 'infection', 'cell_id', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'doublet_score', 'predicted_doublet', 'scDblFinder_score', 'scDblFinder_class', 'gem', 'QC', 'n_genes', 'S_score', 'G2M_score', 'phase'
var: 'mt', 'ribo', 'n_cells_by_counts-gem1', 'mean_counts-gem1', 'log1p_mean_counts-gem1', 'pct_dropout_by_counts-gem1', 'total_counts-gem1', 'log1p_total_counts-gem1', 'n_cells_by_counts-gem2', 'mean_counts-gem2', 'log1p_mean_counts-gem2', 'pct_dropout_by_counts-gem2', 'total_counts-gem2', 'log1p_total_counts-gem2', 'n_cells', 'n_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'group_colors', 'hvg', 'log1p', 'pca'
obsm: 'X_pca'
varm: 'PCs'
layers: 'counts', 'soupX_counts'
Optimize Nearest Neighbors¶
Write a function to automate iteration of nearest neighbor analysis:
InĀ [4]:
# Define a function to automate the iteration of different neighbor values, holding PC constant.
def iterate_neighbors(adata_local, pcs = 25, neighbors = 10, min = 0, max = 11):
# Loop over different nearest neighbor values based on provided min and max values
for index in range(min, max):
# Calculate nearest neighbors with n_neighbors of neighbors + index
adata_mod = sc.pp.neighbors(adata_local, n_neighbors = neighbors + index, n_pcs = pcs, copy = True)
# Do leiden clustering from neighborhood graph
sc.tl.leiden(adata_mod)
# Initialize the PAGA
sc.tl.paga(adata_mod)
sc.pl.paga(adata_mod, title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
# Do a UMAP based on initialized PAGA graph
sc.tl.umap(adata_mod, init_pos='paga')
# Plot UMAP annotated by leiden clusters and original identity
sc.pl.umap(adata_mod, color = "group", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
sc.pl.umap(adata_mod, color = "leiden", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
# Get leiden clusters and original identities
obs_df = sc.get.obs_df(adata_mod, ["group", "leiden"])
# Print tapply
print(obs_df.groupby("group").value_counts().unstack())
del(adata_mod) # Cleanup
# End of loop
del(adata_local)
# End of function
25 PCs, neigbhor 3 to 18¶
InĀ [5]:
iterate_neighbors(adata, pcs = 25, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:20)
running Leiden clustering
finished: found 51 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 41 42 43 \ group ... Base 6 1 6 20 377 393 20 523 119 528 ... 26 2 0 Naive 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 Null 0 0 23 1 357 283 47 282 618 339 ... 18 5 0 WT 25 1545 33 136 46 71 21 82 46 35 ... 16 0 0 d5 3 2 2 1 23 19 6 4 2 6 ... 1 0 19 d8 6 0 0 5 242 95 7 51 64 84 ... 1 0 0 dAD 8 0 1315 45 46 94 902 63 123 29 ... 13 24 0 dID 1679 9 17 33 62 75 28 47 73 42 ... 13 3 5 dVWRPY 17 42 67 979 37 74 61 38 40 20 ... 5 0 0 leiden 44 45 46 47 48 49 50 group Base 0 0 0 0 1 0 0 Naive 0 0 0 0 0 3 0 Null 0 0 0 1 2 0 2 WT 0 0 1 0 0 0 0 d5 0 6 0 0 0 0 0 d8 0 0 0 0 0 0 0 dAD 17 0 0 2 0 0 1 dID 0 0 0 0 0 0 0 dVWRPY 1 1 3 1 0 0 0 [9 rows x 51 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 25 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 15 16 \ group ... Base 9 679 3 20 11 460 546 742 584 19 ... 265 0 Naive 0 0 0 0 0 0 0 0 0 0 ... 1 542 Null 27 1214 0 0 5 828 374 557 397 7 ... 118 0 WT 45 85 2295 37 244 65 177 69 77 673 ... 66 0 d5 3 15 3 6 7 9 34 7 21 17 ... 12 0 d8 1 129 0 14 4 102 137 101 305 4 ... 194 0 dAD 2484 219 1 8 78 120 134 80 63 37 ... 32 0 dID 27 121 14 2114 60 130 211 59 90 63 ... 114 0 dVWRPY 97 77 59 36 1708 67 108 38 42 755 ... 44 0 leiden 17 18 19 20 21 22 23 24 group Base 8 33 35 29 3 0 9 1 Naive 0 0 0 0 1 0 0 0 Null 1 33 17 38 11 0 21 0 WT 279 76 30 29 8 0 2 0 d5 1 6 4 2 39 94 1 0 d8 3 19 5 1 11 0 10 0 dAD 5 28 9 20 16 0 4 0 dID 12 27 67 21 11 0 7 1 dVWRPY 110 56 21 8 15 1 7 2 [9 rows x 25 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 19 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 941 5 824 10 21 797 15 486 659 4 17 32 124 Naive 0 0 0 0 0 1 0 0 0 0 0 0 0 Null 1485 1 608 7 2 483 49 851 807 13 7 42 74 WT 168 2928 244 43 344 104 36 59 92 24 248 30 275 d5 19 7 36 6 10 34 3 11 6 1 13 746 22 d8 148 0 174 9 11 514 3 126 64 0 13 79 18 dAD 230 4 186 9 87 90 1760 132 75 1531 45 30 66 dID 156 22 230 2374 65 170 30 144 76 14 43 54 219 dVWRPY 99 116 197 41 1936 61 78 80 42 47 719 42 163 leiden 13 14 15 16 17 18 group Base 205 0 31 2 23 1 Naive 0 542 0 1 0 0 Null 87 0 17 11 21 0 WT 124 0 30 8 14 59 d5 5 0 4 45 1 0 d8 33 0 5 11 1 0 dAD 59 0 9 13 22 3 dID 316 0 63 11 22 2 dVWRPY 44 0 21 16 9 20 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 18 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 953 5 6 621 26 7 968 584 598 18 22 189 12 Naive 0 0 0 0 0 0 0 1 0 0 0 0 0 Null 1574 0 27 1328 7 0 615 330 426 6 36 74 35 WT 147 2915 42 114 391 43 77 169 94 247 26 131 20 d5 17 6 3 20 8 7 9 36 25 15 749 5 7 d8 164 0 3 155 10 12 136 192 379 11 75 34 7 dAD 203 4 2577 218 85 8 75 93 81 32 29 54 790 dID 155 29 27 185 87 2240 77 240 124 53 49 454 24 dVWRPY 91 98 83 99 1943 31 47 135 38 835 47 45 80 leiden 13 14 15 16 17 group Base 129 0 32 3 24 Naive 0 542 0 1 0 Null 54 0 17 12 24 WT 359 0 28 8 19 d5 16 0 3 42 1 d8 13 0 5 12 1 dAD 63 0 10 13 16 dID 173 0 60 12 22 dVWRPY 112 0 21 16 10 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 19 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 797 487 10 749 633 1 25 3 13 905 13 167 Naive 0 0 0 0 0 0 0 0 0 0 0 1 Null 1263 1217 2 679 576 0 8 21 2 514 42 37 WT 124 90 42 88 210 2151 224 26 1043 67 42 269 d5 15 16 5 28 39 3 8 1 13 9 5 6 d8 98 145 12 445 197 0 8 2 10 95 5 58 dAD 136 196 8 95 164 0 97 1898 24 51 1495 29 dID 124 159 2281 132 244 4 62 17 61 58 31 81 dVWRPY 64 90 32 49 172 27 1615 57 772 46 77 510 leiden 12 13 14 15 16 17 18 group Base 24 196 116 0 31 3 24 Naive 0 0 0 542 0 1 0 Null 40 79 34 0 17 11 23 WT 26 107 273 0 26 8 14 d5 755 6 15 0 4 40 1 d8 73 34 9 0 5 12 1 dAD 31 51 37 0 9 13 17 dID 51 450 175 0 55 11 15 dVWRPY 47 41 87 0 21 16 8 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 11 8 18 827 824 9 1158 650 327 21 209 11 64 Naive 0 0 0 0 1 0 0 0 0 0 0 0 0 Null 38 0 3 1320 630 3 851 625 878 36 93 4 34 WT 56 3073 426 140 227 39 111 88 79 24 130 170 217 d5 6 8 10 12 36 4 9 27 19 766 7 8 16 d8 4 1 15 131 224 14 149 397 128 80 35 4 9 dAD 3245 7 86 167 265 9 98 92 191 29 61 20 43 dID 33 25 87 132 251 2445 95 114 173 45 326 34 169 dVWRPY 102 118 2228 75 221 33 50 43 102 46 44 540 84 leiden 13 14 15 16 group Base 0 32 2 26 Naive 542 0 1 0 Null 0 17 11 22 WT 0 26 8 16 d5 0 4 36 1 d8 0 5 12 1 dAD 0 9 13 16 dID 0 55 11 16 dVWRPY 0 21 16 8 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 10 3 868 570 760 15 22 808 776 18 24 200 63 Naive 0 0 0 0 1 0 0 0 0 0 0 0 0 Null 33 0 1419 1320 581 4 7 609 412 6 30 71 21 WT 53 2937 139 106 215 38 348 103 85 365 25 118 249 d5 5 7 14 17 40 7 8 34 12 13 751 3 16 d8 1 0 128 174 242 16 6 440 65 10 67 34 8 dAD 3214 1 164 206 324 7 79 95 59 50 28 56 30 dID 33 16 157 199 268 2484 83 113 44 56 41 300 134 dVWRPY 96 87 77 94 206 33 1896 51 40 942 45 44 74 leiden 13 14 15 16 group Base 0 31 2 27 Naive 542 0 1 0 Null 0 17 11 24 WT 0 26 8 15 d5 0 4 36 2 d8 0 5 12 1 dAD 0 9 13 16 dID 0 56 11 16 dVWRPY 0 21 16 9 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 887 1091 687 1008 5 19 11 18 5 23 14 167 Naive 0 0 0 1 0 0 0 0 0 0 0 0 Null 1380 862 1351 702 26 6 5 3 0 35 22 42 WT 138 102 100 219 39 349 39 1539 1799 25 17 299 d5 16 31 20 43 1 11 6 19 1 755 4 17 d8 131 477 184 244 0 7 15 6 0 79 3 9 dAD 153 104 209 165 2630 88 6 27 1 30 803 41 dID 149 126 187 253 24 84 2515 46 7 43 12 190 dVWRPY 75 53 99 194 80 2141 44 743 40 44 51 76 leiden 12 13 14 15 16 group Base 201 0 32 27 2 Naive 0 542 0 0 1 Null 79 0 17 24 11 WT 109 0 27 21 8 d5 5 0 4 2 34 d8 36 0 5 1 12 dAD 56 0 9 16 13 dID 289 0 59 16 11 dVWRPY 44 0 21 10 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 1278 1521 12 12 18 52 996 25 212 0 11 31 27 2 Naive 0 0 0 0 0 0 1 0 0 542 0 0 0 1 Null 2438 1267 1 32 7 8 606 40 94 0 19 17 25 11 WT 285 321 3265 59 447 59 107 30 124 0 75 27 23 8 d5 30 45 12 8 12 7 34 768 6 0 8 4 1 34 d8 251 298 1 2 12 41 460 84 36 0 6 5 1 12 dAD 277 405 4 3279 101 11 115 43 55 0 21 10 17 13 dID 291 362 41 35 93 2516 146 45 323 0 72 56 20 11 dVWRPY 158 247 242 116 2672 43 57 48 47 0 54 21 10 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1409 1711 5 19 582 35 3 75 30 203 63 0 Naive 0 0 0 0 0 0 0 1 0 0 0 542 Null 1211 1532 23 7 1566 9 0 13 38 88 23 0 WT 281 185 50 405 128 38 2188 1096 31 122 248 0 d5 48 37 3 10 12 5 1 18 768 8 16 0 d8 281 536 0 10 179 37 0 13 89 39 7 0 dAD 655 160 3024 96 210 10 1 21 37 67 30 0 dID 349 171 30 99 219 2505 5 68 47 308 121 0 dVWRPY 263 94 88 2451 111 42 40 429 52 44 70 0 leiden 12 13 14 group Base 32 27 3 Naive 0 0 1 Null 17 26 12 WT 27 23 8 d5 4 1 38 d8 5 1 12 dAD 10 17 13 dID 59 18 12 dVWRPY 21 10 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1409 1275 8 4 12 42 826 245 12 30 188 87 Naive 1 0 0 0 0 0 0 0 0 0 0 0 Null 1166 1744 1 29 6 12 540 865 1 37 74 38 WT 267 157 3145 48 46 458 97 57 129 33 123 216 d5 47 20 5 2 8 22 25 10 2 770 4 15 d8 271 178 0 1 18 18 453 126 0 84 33 9 dAD 588 174 3 3054 9 86 98 113 31 39 57 60 dID 329 136 27 30 2540 83 108 99 38 51 281 206 dVWRPY 240 84 146 97 39 1726 43 66 1066 54 42 81 leiden 12 13 14 15 group Base 0 31 26 2 Naive 542 0 0 1 Null 0 17 24 11 WT 0 27 19 8 d5 0 4 1 34 d8 0 5 1 12 dAD 0 10 16 13 dID 0 55 17 11 dVWRPY 0 21 11 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1431 1383 5 26 14 936 41 3 30 192 0 76 32 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2414 1302 25 7 4 623 8 1 37 62 0 28 17 WT 226 278 46 310 43 104 1381 2040 31 113 0 201 27 d5 26 47 1 8 8 32 20 0 768 4 0 16 4 d8 272 274 0 7 13 484 13 0 85 35 0 7 5 dAD 273 654 3023 97 6 103 36 1 39 52 0 28 9 dID 270 337 25 87 2497 135 71 7 50 309 0 138 54 dVWRPY 136 263 81 2091 37 49 856 44 49 42 0 34 21 leiden 13 14 group Base 26 2 Naive 0 1 Null 26 11 WT 22 8 d5 0 35 d8 2 12 dAD 17 13 dID 20 11 dVWRPY 12 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1265 17 1284 9 664 24 18 557 25 200 72 0 32 Naive 1 0 0 0 0 0 0 0 0 0 0 542 0 Null 959 3 1110 26 1620 8 5 641 41 71 27 0 17 WT 291 3304 129 49 115 381 46 98 29 118 212 0 28 d5 57 15 31 2 15 8 7 12 757 5 13 0 4 d8 276 1 501 1 209 9 20 52 80 35 7 0 5 dAD 440 9 147 3202 201 104 6 78 39 54 32 0 9 dID 343 49 154 23 185 99 2537 75 43 279 138 0 55 dVWRPY 371 406 62 91 104 2410 41 48 55 47 48 0 21 leiden 13 14 group Base 27 3 Naive 0 1 Null 26 11 WT 22 8 d5 2 41 d8 1 12 dAD 17 13 dID 19 12 dVWRPY 11 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1269 1176 17 5 1027 17 2 210 26 28 180 180 Naive 1 0 0 0 0 0 0 0 0 0 0 0 Null 963 1862 2 16 762 4 0 738 13 37 60 58 WT 283 149 1529 44 101 42 1989 36 101 30 357 110 d5 50 21 19 0 32 7 3 6 4 768 17 3 d8 274 198 6 0 480 12 0 87 5 81 15 33 dAD 611 204 51 3029 115 5 0 93 67 36 48 53 dID 336 162 82 25 138 2449 8 95 52 47 210 308 dVWRPY 403 87 1802 80 60 31 106 40 901 47 85 39 leiden 12 13 14 15 group Base 0 32 26 2 Naive 542 0 0 1 Null 0 17 22 11 WT 0 29 22 8 d5 0 4 0 35 d8 0 5 1 12 dAD 0 9 17 13 dID 0 55 33 11 dVWRPY 0 21 13 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 13 1200 1431 9 1075 14 161 28 206 0 32 26 2 Naive 0 0 1 0 0 0 0 0 0 542 0 0 1 Null 3 2214 1180 28 901 3 52 42 87 0 17 27 11 WT 3504 156 291 50 123 46 450 29 124 0 28 21 8 d5 22 21 48 2 34 8 22 767 5 0 4 1 35 d8 4 246 305 0 481 20 17 82 35 0 5 2 12 dAD 38 226 417 3271 133 6 119 39 63 0 9 17 13 dID 63 213 347 29 147 2506 262 44 315 0 55 19 11 dVWRPY 1675 110 361 89 57 45 1254 48 44 0 21 11 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1137 1358 10 2 21 1142 18 29 222 15 182 0 32 Naive 0 1 0 0 0 0 0 0 0 0 0 542 0 Null 2195 1175 24 0 5 922 5 37 78 4 68 0 17 WT 151 253 53 2979 457 120 43 31 314 253 119 0 27 d5 22 47 2 4 13 30 7 770 18 12 5 0 4 d8 240 299 1 0 9 486 16 85 18 6 31 0 5 dAD 248 268 3377 1 94 131 9 37 67 27 53 0 9 dID 203 334 29 15 73 132 2599 46 237 37 222 0 54 dVWRPY 118 179 100 95 2362 57 34 47 87 558 44 0 21 leiden 13 14 group Base 27 2 Naive 0 1 Null 24 11 WT 22 8 d5 1 34 d8 1 12 dAD 17 13 dID 19 11 dVWRPY 13 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:07)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1240 1322 6 6 1133 10 30 15 29 167 180 0 Naive 0 1 0 0 0 0 0 0 0 0 0 542 Null 2330 1178 1 21 821 4 10 5 37 47 61 0 WT 157 253 2453 46 117 46 154 1108 30 301 114 0 d5 23 48 7 2 32 8 10 15 763 17 5 0 d8 257 294 2 1 491 11 5 5 84 8 33 0 dAD 249 400 24 3229 125 6 123 15 40 45 57 0 dID 226 336 37 24 147 2527 67 45 44 200 276 0 dVWRPY 116 182 1231 79 68 39 1412 400 51 67 43 0 leiden 12 13 14 group Base 31 2 26 Naive 0 1 0 Null 17 11 22 WT 26 8 17 d5 4 35 0 d8 5 12 1 dAD 9 13 16 dID 54 11 17 dVWRPY 21 16 6 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:06)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:13)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:16)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1282 1234 11 1179 11 0 29 10 29 150 202 0 Naive 0 1 0 0 0 0 0 0 0 0 0 542 Null 2319 1222 20 766 5 0 6 4 38 48 86 0 WT 163 222 49 138 40 2549 778 355 32 336 115 0 d5 21 50 1 28 7 3 20 7 768 17 8 0 d8 257 311 0 469 16 0 10 4 81 9 34 0 dAD 254 431 3220 130 7 0 93 40 37 43 58 0 dID 226 338 30 133 2536 7 74 45 47 203 288 0 dVWRPY 132 155 101 61 30 62 1335 1622 55 87 44 0 leiden 12 13 14 group Base 31 27 2 Naive 0 0 1 Null 17 23 11 WT 27 18 8 d5 4 1 34 d8 5 1 12 dAD 9 16 13 dID 54 19 11 dVWRPY 21 10 16
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
30 PCs, neigbhor 3 to 18¶
InĀ [6]:
iterate_neighbors(adata, pcs = 30, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 48 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 38 39 \ group ... Base 7 2 588 20 5 429 14 5 318 19 ... 1 33 Naive 0 0 0 0 0 1 0 0 0 0 ... 1 0 Null 19 1 576 2 1 295 9 0 310 29 ... 11 7 WT 26 1622 99 27 171 105 206 1024 61 21 ... 7 7 d5 1 7 23 4 6 42 14 2 16 3 ... 20 3 d8 1 0 88 10 0 95 16 0 240 1 ... 12 3 dAD 1914 0 67 2 30 83 57 0 39 787 ... 12 2 dID 8 18 84 1409 41 98 57 26 66 21 ... 11 28 dVWRPY 68 95 43 20 1137 71 755 44 27 42 ... 15 4 leiden 40 41 42 43 44 45 46 47 group Base 17 1 0 0 3 3 0 0 Naive 0 0 0 0 0 0 3 0 Null 12 1 0 0 0 0 0 2 WT 17 2 0 0 1 0 0 0 d5 0 0 8 7 0 0 0 0 d8 1 0 0 0 0 0 0 0 dAD 10 0 0 0 0 0 0 0 dID 15 0 0 0 0 0 0 1 dVWRPY 6 4 0 1 0 0 0 0 [9 rows x 48 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 26 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 16 17 \ group ... Base 11 4 816 2 521 836 16 291 509 12 ... 173 191 Naive 0 0 0 0 0 0 0 0 0 0 ... 0 0 Null 7 0 1031 21 515 564 4 802 387 4 ... 74 107 WT 37 2279 109 31 144 58 212 62 77 934 ... 120 221 d5 5 4 26 3 41 13 6 2 20 13 ... 3 12 d8 17 0 111 0 134 143 11 96 277 5 ... 33 18 dAD 8 1 99 2051 153 65 40 166 60 8 ... 51 45 dID 2276 14 78 15 163 68 52 105 87 64 ... 332 194 dVWRPY 27 73 42 48 116 31 1305 55 36 302 ... 59 34 leiden 18 19 20 21 22 23 24 25 group Base 0 2 14 31 29 2 0 0 Naive 542 0 0 0 0 1 0 0 Null 0 115 8 17 23 11 0 0 WT 0 3 49 27 35 8 0 0 d5 0 1 1 4 1 41 98 7 d8 0 3 4 5 1 12 0 0 dAD 0 44 22 10 17 13 0 0 dID 0 9 24 49 21 11 0 0 dVWRPY 0 3 51 21 12 15 0 1 [9 rows x 26 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 20 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 8 862 25 1098 14 675 446 16 24 0 353 224 Naive 0 0 0 0 0 0 0 0 0 0 0 0 Null 0 1583 10 736 46 561 981 3 9 12 249 108 WT 3106 132 39 90 45 192 82 268 240 13 54 135 d5 11 23 7 17 7 47 11 3 17 1 14 8 d8 3 173 28 180 5 179 114 5 9 0 253 38 dAD 3 206 10 110 2143 175 151 73 87 1094 48 75 dID 41 157 2399 115 38 213 135 60 76 4 50 320 dVWRPY 175 80 20 52 95 127 82 1501 1257 33 26 57 leiden 12 13 14 15 16 17 18 19 group Base 27 97 264 0 34 28 2 0 Naive 0 0 1 542 0 0 1 0 Null 41 36 137 0 18 24 11 0 WT 31 294 36 0 29 36 8 0 d5 623 14 9 0 4 1 41 111 d8 82 12 110 0 5 1 12 0 dAD 41 54 41 0 10 17 13 0 dID 51 209 62 0 45 25 11 0 dVWRPY 62 88 26 0 20 14 15 1 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 18 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1108 17 25 931 9 1002 4 483 18 34 203 141 Naive 0 0 0 0 0 0 0 0 0 0 0 0 Null 1707 2 5 739 5 697 19 1062 42 44 105 32 WT 175 3158 426 223 39 95 34 79 36 34 126 254 d5 23 15 11 47 6 30 3 10 5 750 4 13 d8 194 4 7 182 11 427 0 124 7 84 38 10 dAD 191 5 92 185 8 96 2346 191 1012 42 61 40 dID 180 62 74 234 2433 122 12 154 33 52 309 186 dVWRPY 104 332 2485 197 35 50 80 75 116 61 45 35 leiden 12 13 14 15 16 17 group Base 0 147 15 32 26 2 Naive 542 1 0 0 0 1 Null 0 35 17 17 26 11 WT 0 20 69 29 25 8 d5 0 4 2 4 1 41 d8 0 96 7 5 1 12 dAD 0 18 24 10 17 13 dID 0 52 27 51 19 11 dVWRPY 0 14 53 20 14 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1036 10 10 883 7 21 907 20 658 231 30 209 114 Naive 0 0 0 1 0 0 0 0 0 0 0 0 0 Null 1780 51 1 781 5 8 584 5 430 686 47 104 30 WT 164 51 3008 220 31 261 65 352 88 50 31 130 318 d5 18 4 7 36 4 5 10 17 22 6 767 4 19 d8 193 3 2 232 12 6 141 15 380 83 77 39 7 dAD 209 3242 2 252 6 89 87 80 82 117 37 60 48 dID 176 32 29 271 2425 62 78 67 120 124 51 308 190 dVWRPY 83 101 113 183 27 1561 46 1286 38 71 45 44 84 leiden 13 14 15 16 group Base 0 31 27 3 Naive 542 0 0 1 Null 0 17 24 12 WT 0 29 24 8 d5 0 4 1 45 d8 0 5 1 13 dAD 0 10 17 13 dID 0 41 24 13 dVWRPY 0 20 14 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1222 9 1194 24 20 6 783 550 3 25 213 87 Naive 0 0 0 0 0 0 0 1 0 0 0 0 Null 2038 48 1378 5 4 4 495 369 0 44 102 25 WT 195 52 154 386 1747 27 99 156 1562 27 102 269 d5 22 4 19 9 18 6 29 29 0 762 5 16 d8 216 3 177 10 7 14 490 147 0 78 37 11 dAD 256 3299 209 98 23 7 98 170 1 39 70 41 dID 212 34 217 98 65 2450 131 196 2 47 308 169 dVWRPY 113 102 130 2158 769 26 41 145 48 45 42 67 leiden 12 13 14 15 group Base 0 31 2 28 Naive 542 0 1 0 Null 0 17 12 24 WT 0 27 8 19 d5 0 4 45 1 d8 0 5 13 1 dAD 0 10 13 17 dID 0 49 13 20 dVWRPY 0 20 15 10 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1480 1379 10 5 22 10 846 29 203 151 0 31 27 Naive 0 0 0 0 0 0 1 0 0 0 542 0 0 Null 2533 1209 3 28 5 5 552 44 95 38 0 17 24 WT 234 296 3243 44 423 34 107 32 122 236 0 27 24 d5 24 50 10 2 13 6 28 763 5 19 0 4 1 d8 283 278 3 2 9 25 457 83 36 14 0 5 1 dAD 280 616 6 3057 88 9 106 39 59 51 0 9 18 dID 271 337 42 28 84 2481 114 51 306 196 0 50 38 dVWRPY 136 397 288 111 2502 34 51 47 45 64 0 21 20 leiden 13 group Base 4 Naive 1 Null 12 WT 8 d5 44 d8 13 dAD 13 dID 13 dVWRPY 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1466 1519 10 8 24 10 805 30 189 0 74 31 27 Naive 0 0 0 0 0 0 1 0 0 542 0 0 0 Null 2490 1329 3 44 7 5 475 42 93 0 25 17 23 WT 238 290 3294 55 417 32 97 31 113 0 203 27 25 d5 25 59 11 2 11 7 27 759 4 0 16 4 1 d8 285 299 1 1 12 18 445 84 36 0 9 5 1 dAD 301 411 4 3238 119 5 103 39 62 0 29 9 18 dID 291 365 45 28 103 2453 118 51 327 0 128 55 34 dVWRPY 137 306 270 105 2655 29 48 46 45 0 40 21 13 leiden 13 group Base 4 Naive 1 Null 12 WT 8 d5 43 d8 13 dAD 13 dID 13 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1475 1659 6 621 4 16 13 126 31 182 0 30 27 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1175 1460 26 1689 0 3 7 31 47 66 0 17 24 WT 304 182 40 104 2795 763 37 371 31 104 0 29 24 d5 63 37 0 17 4 16 7 16 759 4 0 4 2 d8 320 521 2 174 0 12 23 9 91 35 0 5 2 dAD 607 163 3016 221 2 53 8 130 38 53 0 10 18 dID 356 144 27 208 23 63 2488 228 51 305 0 55 34 dVWRPY 322 76 69 79 60 1816 30 1107 47 40 0 21 14 leiden 13 14 group Base 5 2 Naive 0 1 Null 9 11 WT 38 8 d5 1 39 d8 3 12 dAD 19 13 dID 18 11 dVWRPY 35 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1524 1172 6 7 30 1167 12 33 180 0 32 26 5 Naive 0 1 0 0 0 0 0 0 0 542 0 0 0 Null 2439 1084 1 40 10 794 6 44 82 0 18 25 11 WT 325 305 3330 57 406 127 36 35 119 0 28 27 27 d5 30 68 11 1 13 28 9 752 7 0 4 3 1 d8 278 255 0 2 8 503 18 89 34 0 5 1 4 dAD 275 410 4 3250 126 126 8 39 54 0 10 18 18 dID 337 398 40 26 108 143 2481 49 308 0 56 34 20 dVWRPY 139 257 231 105 2734 55 32 47 46 0 21 16 32 leiden 13 group Base 3 Naive 1 Null 11 WT 8 d5 42 d8 12 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1253 1296 22 9 1295 38 10 1 31 179 0 31 25 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2291 1133 4 30 902 12 5 0 42 87 0 17 23 WT 243 320 2143 45 130 372 31 1282 33 102 0 26 35 d5 23 64 21 1 34 10 7 1 764 4 0 3 2 d8 236 262 8 2 528 8 22 0 88 34 0 5 2 dAD 267 570 40 3066 145 102 7 1 39 57 0 10 18 dID 274 389 69 24 157 153 2466 7 48 307 0 53 37 dVWRPY 103 269 1058 94 62 1896 25 45 48 40 0 21 21 leiden 13 14 group Base 5 2 Naive 0 1 Null 8 11 WT 60 8 d5 1 34 d8 2 12 dAD 16 13 dID 16 11 dVWRPY 33 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1470 1220 6 1160 19 10 33 1 31 178 0 32 9 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2482 1039 32 808 4 4 8 0 42 80 0 18 11 WT 274 336 45 113 1446 29 281 2072 33 101 0 26 39 d5 23 63 2 31 21 8 8 0 768 4 0 4 1 d8 281 243 3 502 10 17 6 0 91 34 0 5 4 dAD 285 347 3269 136 43 5 106 1 40 56 0 10 22 dID 327 402 25 139 64 2474 91 11 48 306 0 53 26 dVWRPY 121 248 73 55 1176 25 1801 45 46 41 0 21 43 leiden 13 14 group Base 26 2 Naive 0 1 Null 26 11 WT 27 8 d5 1 35 d8 1 12 dAD 18 13 dID 34 11 dVWRPY 21 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1361 1182 4 1263 22 16 78 1 28 175 0 32 28 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2446 1044 32 824 5 7 18 0 43 83 0 17 26 WT 212 256 48 121 1327 29 487 2131 34 98 0 28 26 d5 24 55 0 33 26 8 12 0 767 4 0 3 2 d8 248 231 0 548 10 18 10 0 91 33 0 5 1 dAD 254 485 3138 145 68 5 103 1 41 56 0 10 19 dID 258 343 23 167 82 2484 189 7 49 298 0 50 35 dVWRPY 115 218 93 60 1377 24 1632 37 48 41 0 21 23 leiden 13 14 group Base 2 5 Naive 1 0 Null 11 9 WT 8 25 d5 34 1 d8 12 2 dAD 13 13 dID 11 15 dVWRPY 16 26 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1549 1227 4 4 8 19 796 15 304 30 174 0 31 Naive 0 0 0 0 0 0 1 0 0 0 0 542 0 Null 1619 1077 28 1 5 6 486 5 1174 40 62 0 17 WT 330 269 44 2582 24 269 97 939 66 30 96 0 28 d5 30 58 0 1 8 6 31 20 11 754 4 0 3 d8 225 251 0 0 19 4 474 6 82 92 33 0 5 dAD 221 559 3056 2 5 97 103 38 118 39 54 0 9 dID 304 331 21 14 2521 78 109 64 134 47 292 0 49 dVWRPY 129 239 90 76 26 1983 40 944 34 47 41 0 21 leiden 13 14 15 group Base 6 27 3 Naive 0 0 1 Null 9 25 11 WT 30 18 8 d5 1 2 40 d8 4 2 12 dAD 20 17 13 dID 19 17 11 dVWRPY 37 9 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1318 1483 5 10 25 987 0 22 31 183 72 0 32 Naive 0 1 0 0 0 0 0 0 0 0 0 542 0 Null 2379 1286 27 4 8 656 0 4 43 86 21 0 17 WT 217 282 45 29 300 100 2311 1121 32 98 237 0 27 d5 19 54 0 8 7 32 0 23 766 4 17 0 3 d8 253 300 0 22 5 473 0 8 89 34 7 0 5 dAD 253 544 3117 7 117 111 1 41 39 53 27 0 9 dID 263 362 23 2526 90 116 6 68 51 276 144 0 41 dVWRPY 114 239 85 23 2021 53 43 966 46 40 49 0 21 leiden 13 14 group Base 27 2 Naive 0 1 Null 23 11 WT 23 8 d5 1 35 d8 1 12 dAD 19 13 dID 34 11 dVWRPY 15 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1627 1401 5 2 22 9 835 23 29 179 0 32 2 Naive 0 0 0 0 0 0 1 0 0 0 542 0 1 Null 2593 1267 31 0 6 5 490 8 41 63 0 18 12 WT 345 311 50 2675 298 26 95 823 32 98 0 28 8 d5 24 55 2 0 9 8 29 20 765 4 0 3 47 d8 293 258 4 0 4 21 471 7 93 37 0 5 13 dAD 294 363 3302 1 116 8 92 29 38 56 0 10 13 dID 356 389 27 11 103 2523 109 64 46 288 0 51 13 dVWRPY 152 215 94 74 2141 32 40 825 48 41 0 21 17 leiden 13 14 group Base 26 5 Naive 0 0 Null 23 8 WT 18 23 d5 2 1 d8 1 2 dAD 17 12 dID 17 14 dVWRPY 8 23 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1384 1259 5 27 1 7 725 20 505 29 169 0 32 Naive 0 0 0 0 0 0 0 0 1 0 0 542 0 Null 2214 1366 25 6 0 4 464 5 316 44 62 0 17 WT 306 224 47 347 2548 25 84 904 142 32 95 0 28 d5 24 26 3 9 0 8 25 20 33 765 3 0 3 d8 248 186 1 6 0 19 411 5 194 85 33 0 5 dAD 254 292 3214 118 1 8 84 27 218 37 46 0 10 dID 304 309 19 95 11 2506 91 59 200 50 283 0 41 dVWRPY 133 122 85 2215 54 28 33 773 130 50 40 0 21 leiden 13 14 15 group Base 3 25 6 Naive 1 0 0 Null 12 23 7 WT 8 18 22 d5 47 2 1 d8 13 1 2 dAD 13 17 12 dID 13 17 13 dVWRPY 16 8 23 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:15)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1366 6 1280 6 26 6 791 452 24 169 0 32 27 Naive 0 0 0 0 0 0 0 1 0 0 542 0 0 Null 2170 3 1434 25 4 4 512 243 45 61 0 17 23 WT 294 3412 242 48 338 26 95 138 31 106 0 28 33 d5 21 17 31 3 12 7 28 32 763 4 0 5 2 d8 236 1 198 4 8 14 464 155 74 33 0 5 1 dAD 251 12 272 3326 124 6 98 116 37 45 0 9 19 dID 288 39 332 22 103 2473 118 178 45 291 0 51 37 dVWRPY 119 653 140 93 2312 33 40 147 48 43 0 21 16 leiden 13 14 group Base 9 3 Naive 0 1 Null 13 11 WT 31 8 d5 1 43 d8 4 12 dAD 23 13 dID 23 11 dVWRPY 50 16
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
35 PCs, neigbhor 3 to 18¶
InĀ [7]:
iterate_neighbors(adata, pcs = 35, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 48 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 38 39 \ group ... Base 8 8 25 12 198 436 5 0 244 405 ... 3 44 Naive 0 0 0 0 0 0 0 0 0 0 ... 1 0 Null 3 29 4 0 677 481 40 0 563 263 ... 11 7 WT 37 25 156 1052 43 56 27 1127 38 45 ... 8 7 d5 2 0 6 0 2 5 2 0 6 19 ... 32 10 d8 13 0 6 4 91 40 0 0 82 248 ... 11 8 dAD 4 1317 76 4 98 61 1041 0 93 44 ... 13 3 dID 1592 14 51 34 59 56 19 2 74 60 ... 10 3 dVWRPY 34 65 928 102 22 42 43 9 34 28 ... 16 2 leiden 40 41 42 43 44 45 46 47 group Base 0 0 0 0 0 0 0 0 Naive 0 0 0 0 3 0 0 0 Null 0 0 4 0 0 0 0 0 WT 0 0 0 0 0 1 0 0 d5 81 7 0 4 0 0 0 1 d8 0 0 0 0 0 0 0 1 dAD 0 0 0 0 0 0 0 0 dID 0 0 0 0 0 1 0 1 dVWRPY 0 1 0 0 0 1 3 0 [9 rows x 48 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 24 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 14 15 \ group ... Base 826 4 13 679 9 614 558 21 19 54 ... 189 135 Naive 0 0 0 0 0 0 0 0 0 0 ... 0 0 Null 1526 0 46 710 3 972 479 1 6 15 ... 65 31 WT 135 2646 34 173 45 91 64 258 506 130 ... 110 299 d5 10 2 2 44 3 9 18 6 14 4 ... 7 17 d8 142 0 2 145 17 153 310 4 10 12 ... 31 10 dAD 204 3 2397 248 6 122 80 37 37 122 ... 59 44 dID 132 16 25 200 2115 153 106 50 60 58 ... 317 181 dVWRPY 81 74 61 137 44 71 34 1188 855 853 ... 47 43 leiden 16 17 18 19 20 21 22 23 group Base 0 3 35 33 3 22 0 8 Naive 542 0 0 0 1 0 0 0 Null 0 3 25 18 11 17 0 17 WT 0 5 76 28 8 25 0 4 d5 0 1 8 3 47 1 93 1 d8 0 2 6 5 12 1 0 0 dAD 0 2 29 9 13 12 0 3 dID 0 242 29 47 11 16 0 6 dVWRPY 0 3 46 20 16 5 2 0 [9 rows x 24 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 20 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 11 1039 15 994 7 404 12 58 441 461 28 182 369 Naive 0 0 0 0 0 0 0 0 1 0 0 0 0 Null 42 1463 0 824 4 1282 2 23 263 266 48 85 174 WT 45 149 2997 227 37 83 360 180 67 95 32 115 35 d5 3 17 8 44 7 5 10 8 18 17 659 5 10 d8 3 141 0 174 14 160 13 11 275 231 95 30 34 dAD 3010 171 4 432 10 177 53 180 60 50 39 57 26 dID 28 148 41 242 2421 159 55 96 126 70 49 305 35 dVWRPY 79 68 127 248 43 73 1743 986 32 45 49 42 11 leiden 13 14 15 16 17 18 19 group Base 117 0 4 30 3 22 0 Naive 0 542 0 0 1 0 0 Null 39 0 5 17 11 17 0 WT 253 0 99 28 8 20 0 d5 19 0 5 3 39 1 91 d8 9 0 1 5 12 1 0 dAD 42 0 1 10 13 16 0 dID 133 0 18 56 11 18 0 dVWRPY 45 0 94 19 16 10 1 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1089 15 11 1011 1164 26 10 412 26 35 174 166 Naive 0 0 0 0 1 0 0 0 0 0 0 0 Null 1688 49 1 933 723 6 4 941 8 46 62 59 WT 187 50 3070 180 117 320 42 68 304 33 113 283 d5 18 2 1 49 29 11 5 6 18 660 4 22 d8 168 3 0 226 502 9 20 120 7 89 32 15 dAD 209 3149 4 283 125 105 10 151 136 32 47 61 dID 172 31 30 255 158 77 2308 132 64 49 461 194 dVWRPY 98 98 126 128 55 2060 43 75 822 54 42 82 leiden 12 13 14 15 16 group Base 0 30 24 4 0 Naive 542 0 0 1 0 Null 0 17 17 11 0 WT 0 27 28 8 0 d5 0 3 2 39 100 d8 0 5 1 12 0 dAD 0 10 16 13 0 dID 0 50 19 11 0 dVWRPY 0 20 11 16 1 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1016 10 7 946 22 1113 654 11 31 15 191 124 Naive 0 0 0 0 0 1 0 0 0 0 0 0 Null 1667 42 0 771 8 634 1227 6 43 6 65 48 WT 175 47 3057 252 327 109 93 37 38 256 116 264 d5 19 2 2 46 11 26 15 7 765 11 3 19 d8 137 0 1 214 9 485 184 21 90 5 33 12 dAD 229 3082 4 442 124 107 168 8 35 17 50 46 dID 178 26 16 274 87 151 153 2459 50 55 296 194 dVWRPY 90 84 124 205 2234 56 89 33 54 597 41 81 leiden 12 13 14 15 group Base 0 31 3 23 Naive 542 0 1 0 Null 0 17 11 20 WT 0 28 8 23 d5 0 3 39 1 d8 0 5 12 1 dAD 0 10 13 16 dID 0 43 11 18 dVWRPY 0 20 16 7 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1118 12 7 26 838 1117 9 691 28 119 173 0 31 Naive 0 0 0 0 0 0 0 1 0 0 0 542 0 Null 1874 3 26 4 1234 809 2 410 46 43 60 0 17 WT 178 3233 43 379 140 115 44 211 32 284 108 0 29 d5 18 10 2 14 27 26 7 32 764 21 3 0 3 d8 200 2 0 11 180 432 16 223 85 10 31 0 5 dAD 247 6 3023 117 271 131 11 370 37 47 48 0 10 dID 193 36 26 84 196 131 2463 250 47 205 277 0 57 dVWRPY 102 297 91 2551 121 55 37 259 54 74 41 0 20 leiden 13 14 group Base 26 2 Naive 0 1 Null 26 11 WT 26 8 d5 1 41 d8 1 13 dAD 20 13 dID 35 11 dVWRPY 13 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1350 15 1490 9 33 881 8 34 184 134 0 30 26 Naive 0 0 1 0 0 0 0 0 0 0 542 0 0 Null 2411 3 1036 38 7 849 4 43 77 43 0 17 26 WT 224 3302 123 48 401 253 42 37 95 241 0 30 26 d5 20 12 28 2 13 46 7 770 5 19 0 3 1 d8 262 2 558 3 13 202 17 95 31 7 0 5 1 dAD 284 7 157 3193 121 406 10 38 54 40 0 10 18 dID 271 45 180 27 93 286 2506 49 284 182 0 43 34 dVWRPY 140 314 67 101 2597 272 47 53 37 54 0 20 13 leiden 13 group Base 3 Naive 1 Null 11 WT 8 d5 43 d8 13 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1289 1572 8 10 831 20 40 32 16 133 186 0 30 Naive 0 1 0 0 0 0 0 0 0 0 0 542 0 Null 2445 1048 36 0 788 9 10 46 8 44 76 0 17 WT 207 130 46 3052 244 328 48 36 296 280 98 0 30 d5 22 29 1 1 48 11 6 771 11 21 3 0 3 d8 264 545 3 0 198 7 27 99 6 8 33 0 5 dAD 299 155 3148 1 402 124 11 39 28 47 56 0 10 dID 264 184 24 18 255 84 2504 51 60 192 288 0 43 dVWRPY 118 70 92 124 230 2149 34 52 701 73 38 0 20 leiden 13 14 group Base 27 3 Naive 0 1 Null 27 11 WT 27 8 d5 1 41 d8 1 13 dAD 18 13 dID 33 11 dVWRPY 14 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1236 1623 12 877 5 29 24 27 202 102 0 30 27 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1113 1266 3 1916 38 10 6 46 79 35 0 17 25 WT 310 159 3334 155 46 335 53 36 101 232 0 27 34 d5 57 29 11 17 1 14 6 762 5 21 0 3 0 d8 265 514 2 206 1 11 46 97 39 8 0 6 2 dAD 645 155 5 226 3007 124 10 35 57 46 0 10 18 dID 340 159 37 232 23 93 2514 48 296 166 0 54 38 dVWRPY 436 80 338 99 87 2447 40 54 39 61 0 20 14 leiden 13 group Base 3 Naive 1 Null 11 WT 8 d5 43 d8 12 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1463 1345 13 28 5 7 962 29 184 100 0 27 31 Naive 0 0 0 0 0 0 1 0 0 0 542 0 0 Null 2395 1379 0 9 27 4 550 41 71 35 0 26 17 WT 212 304 3332 357 42 49 94 29 112 227 0 38 26 d5 21 61 9 15 2 7 25 761 5 18 0 1 3 d8 262 278 1 12 1 15 486 94 32 8 0 2 5 dAD 263 936 4 124 2750 9 100 35 56 34 0 18 9 dID 255 361 42 100 25 2514 130 50 288 154 0 39 42 dVWRPY 137 252 187 2791 94 31 45 52 40 50 0 16 20 leiden 13 group Base 3 Naive 1 Null 11 WT 8 d5 41 d8 13 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:08)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1439 1332 7 6 8 989 28 26 32 178 91 0 28 Naive 0 0 0 0 0 1 0 0 0 0 0 542 0 Null 1451 2270 0 36 4 590 8 7 43 66 36 0 26 WT 282 185 3117 40 38 98 283 359 31 104 222 0 35 d5 61 19 2 1 6 28 8 11 764 4 19 0 1 d8 291 234 0 1 12 497 8 9 95 33 9 0 2 dAD 679 237 1 2988 7 111 94 67 32 56 38 0 18 dID 357 221 26 26 2504 132 74 78 53 289 163 0 34 dVWRPY 205 112 121 70 22 43 1789 1161 49 39 60 0 24 leiden 13 14 group Base 30 3 Naive 0 1 Null 17 11 WT 28 8 d5 3 42 d8 5 13 dAD 10 13 dID 43 11 dVWRPY 20 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1242 1296 16 1252 4 26 16 30 155 99 0 30 28 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2368 1196 4 771 28 7 6 45 55 29 0 17 28 WT 201 290 3363 123 42 356 46 32 105 201 0 30 33 d5 18 63 9 31 0 13 6 765 4 16 0 3 1 d8 246 267 2 500 0 11 28 101 28 6 0 6 2 dAD 262 865 13 121 2818 98 9 37 47 36 0 10 22 dID 258 339 55 142 21 86 2515 51 283 157 0 58 35 dVWRPY 122 311 637 60 82 2283 33 52 40 58 0 21 16 leiden 13 group Base 3 Naive 1 Null 11 WT 8 d5 40 d8 12 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1371 1187 12 24 6 1180 18 32 187 120 0 30 26 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1287 2179 2 11 36 833 6 45 73 41 0 17 24 WT 264 194 3350 358 45 119 44 34 96 261 0 26 31 d5 56 19 10 14 1 31 6 762 4 19 0 3 3 d8 287 217 1 9 1 507 31 93 34 10 0 5 2 dAD 675 237 3 126 3006 130 9 32 50 42 0 10 18 dID 347 244 43 81 20 150 2503 51 285 183 0 55 38 dVWRPY 227 126 302 2694 84 60 27 52 39 68 0 22 14 leiden 13 group Base 4 Naive 1 Null 11 WT 8 d5 41 d8 12 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1419 1070 11 25 4 1191 91 29 183 116 0 30 26 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1370 2119 0 7 27 839 12 44 64 32 0 17 23 WT 279 186 3364 373 50 125 34 28 110 219 0 26 28 d5 65 17 8 15 2 29 6 766 4 19 0 3 1 d8 293 198 1 10 0 485 71 94 31 7 0 5 2 dAD 673 244 3 112 2998 133 16 36 55 39 0 10 19 dID 348 236 51 104 20 167 2472 51 303 159 0 55 34 dVWRPY 212 120 177 2832 88 60 35 50 41 65 0 21 14 leiden 13 group Base 2 Naive 1 Null 11 WT 8 d5 34 d8 12 dAD 13 dID 11 dVWRPY 16 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:09)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1193 1398 6 3 1150 10 27 21 30 186 113 0 27 Naive 0 1 0 0 0 0 0 0 0 0 0 542 0 Null 2371 1259 31 0 679 7 11 4 44 63 42 0 26 WT 178 263 48 3108 110 41 297 340 31 101 247 0 30 d5 18 68 1 2 28 5 10 14 763 4 18 0 1 d8 247 276 0 0 495 16 8 9 96 35 8 0 2 dAD 261 506 3135 1 121 10 107 41 34 56 37 0 19 dID 265 328 19 22 141 2512 74 64 49 286 163 0 35 dVWRPY 111 194 82 142 56 27 1947 964 53 38 60 0 23 leiden 13 14 group Base 31 2 Naive 0 1 Null 17 11 WT 28 8 d5 3 34 d8 5 12 dAD 10 13 dID 42 11 dVWRPY 20 14 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:08)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1215 1411 10 10 19 1138 9 28 182 116 0 27 30 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2313 1226 0 35 9 779 3 45 61 43 0 23 17 WT 213 279 3346 56 345 118 33 30 95 241 0 39 27 d5 20 65 8 1 16 26 6 768 4 18 0 1 3 d8 254 290 1 0 10 485 13 93 35 9 0 2 5 dAD 263 435 3 3250 109 121 10 35 45 38 0 19 10 dID 270 354 36 27 86 129 2502 49 283 184 0 37 43 dVWRPY 137 222 188 99 2771 61 37 52 37 68 0 24 20 leiden 13 group Base 2 Naive 1 Null 11 WT 8 d5 33 d8 12 dAD 13 dID 11 dVWRPY 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1419 945 1400 8 18 8 7 30 197 106 0 27 30 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1196 1965 1145 0 11 32 3 46 77 38 0 24 17 WT 285 175 150 3361 351 49 37 33 99 217 0 38 27 d5 62 17 30 8 15 0 5 768 4 22 0 1 3 d8 323 195 510 1 11 0 12 93 37 7 0 2 6 dAD 472 236 174 3 124 3169 9 34 47 41 0 19 10 dID 366 225 164 38 88 25 2509 49 281 165 0 38 52 dVWRPY 217 127 80 180 2784 91 34 54 37 67 0 24 21 leiden 13 group Base 2 Naive 1 Null 11 WT 8 d5 34 d8 12 dAD 13 dID 11 dVWRPY 15 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1463 13 876 1437 20 6 7 25 188 103 0 27 30 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1214 2 1933 1175 10 26 3 46 64 39 0 25 17 WT 278 3356 162 153 377 45 30 34 99 222 0 38 28 d5 60 10 17 32 16 0 5 767 4 20 0 1 3 d8 327 2 189 514 10 0 14 90 35 8 0 2 6 dAD 599 3 220 169 122 3060 7 34 54 41 0 19 10 dID 355 50 227 174 81 25 2479 48 291 179 0 39 52 dVWRPY 245 304 114 77 2657 88 28 54 41 69 0 18 21 leiden 13 group Base 2 Naive 1 Null 11 WT 8 d5 34 d8 12 dAD 13 dID 11 dVWRPY 15
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
40 PCs, neigbhor 3 to 18¶
InĀ [8]:
iterate_neighbors(adata, pcs = 40, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 51 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:02)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 41 42 \ group ... Base 13 10 2 11 15 15 180 444 10 412 ... 0 7 Naive 0 0 0 0 0 0 0 0 0 0 ... 0 0 Null 40 4 0 0 21 6 688 510 4 221 ... 0 4 WT 29 250 1410 1088 20 47 56 57 20 62 ... 0 29 d5 2 10 6 3 1 8 4 5 5 12 ... 93 0 d8 3 3 1 2 2 9 52 32 9 244 ... 0 1 dAD 1415 30 0 6 1126 7 120 54 5 39 ... 0 8 dID 22 29 5 32 11 1121 87 38 1001 34 ... 0 19 dVWRPY 57 1197 49 125 38 18 35 25 25 32 ... 1 9 leiden 43 44 45 46 47 48 49 50 group Base 38 0 1 2 0 0 0 0 Naive 0 0 0 0 0 3 0 0 Null 19 0 0 6 0 0 0 0 WT 4 0 11 0 0 0 0 0 d5 2 23 0 0 7 0 0 0 d8 1 0 0 0 0 0 0 0 dAD 4 0 0 0 0 0 0 0 dID 4 0 0 1 0 0 3 3 dVWRPY 4 0 4 0 1 0 0 0 [9 rows x 51 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 28 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 18 19 \ group ... Base 12 12 605 10 9 477 347 4 36 692 ... 0 1 Naive 0 0 0 0 0 0 0 0 0 0 ... 542 0 Null 0 0 872 62 32 571 796 0 10 403 ... 0 1 WT 2789 42 90 32 21 85 56 249 286 57 ... 0 2 d5 7 9 7 4 1 22 26 6 16 5 ... 0 1 d8 0 23 66 6 2 92 105 5 14 83 ... 0 0 dAD 3 9 88 1529 1565 202 149 40 90 60 ... 0 1 dID 36 2083 48 50 4 141 105 38 73 51 ... 0 215 dVWRPY 118 29 42 58 49 87 49 1262 992 31 ... 0 1 leiden 20 21 22 23 24 25 26 27 group Base 32 8 1 3 15 13 0 1 Naive 0 0 0 1 0 0 0 0 Null 17 11 0 11 13 16 0 1 WT 26 49 129 8 32 19 0 6 d5 9 2 0 41 1 0 28 0 d8 6 7 0 12 2 1 0 0 dAD 11 24 1 13 5 8 0 2 dID 49 21 2 10 10 13 0 5 dVWRPY 26 54 41 15 11 4 0 4 [9 rows x 28 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 21 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 11 12 \ group ... Base 10 14 922 950 13 19 634 344 650 13 ... 29 198 Naive 0 0 0 0 0 0 1 0 0 0 ... 0 0 Null 44 0 893 1157 4 7 409 784 383 4 ... 47 64 WT 42 2886 193 131 50 269 126 63 68 348 ... 37 110 d5 3 6 33 14 11 4 32 15 17 17 ... 751 3 d8 4 1 136 139 13 12 256 93 332 7 ... 96 36 dAD 3030 4 328 168 4 84 172 154 62 71 ... 37 53 dID 30 28 184 111 2146 66 241 155 77 62 ... 51 305 dVWRPY 95 102 213 86 36 1616 94 71 27 1087 ... 49 38 leiden 13 14 15 16 17 18 19 20 group Base 123 0 12 1 31 22 3 17 Naive 0 542 0 0 0 0 1 0 Null 20 0 8 0 17 20 11 14 WT 268 0 3 112 24 27 8 32 d5 19 0 0 0 9 0 33 1 d8 9 0 1 0 3 1 12 2 dAD 44 0 0 3 9 16 13 5 dID 169 0 225 2 43 41 11 8 dVWRPY 79 0 1 48 24 11 15 12 [9 rows x 21 columns] computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 19 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1128 6 1192 10 16 20 678 9 338 28 333 105 Naive 0 0 0 0 0 0 0 0 1 0 0 0 Null 1628 50 1106 0 5 7 712 5 196 46 214 440 WT 191 44 157 3045 50 260 80 238 242 30 39 28 d5 15 5 29 6 9 5 18 12 38 742 14 4 d8 184 4 164 1 13 11 286 9 97 95 232 53 dAD 234 3160 288 6 3 80 101 69 123 34 45 72 dID 194 40 195 33 2384 68 92 62 133 49 128 83 dVWRPY 129 107 149 150 34 1696 33 1026 152 47 23 27 leiden 12 13 14 15 16 17 18 group Base 176 83 0 32 24 3 16 Naive 0 0 542 0 0 1 0 Null 67 24 0 17 22 11 15 WT 122 212 0 24 28 8 32 d5 3 19 0 3 0 47 0 d8 34 6 0 5 1 12 2 dAD 49 49 0 11 9 13 5 dID 294 154 0 48 34 12 8 dVWRPY 42 55 0 23 11 15 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 18 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:09)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1246 1226 9 12 9 914 23 18 251 30 179 195 Naive 0 0 0 0 0 1 0 0 0 0 0 0 Null 1989 1104 48 0 2 512 5 7 674 46 44 65 WT 168 265 45 2890 46 100 324 417 45 29 289 119 d5 16 50 1 4 7 25 7 16 9 758 23 3 d8 185 197 1 1 14 520 9 6 109 101 13 32 dAD 231 489 3102 2 5 104 66 68 106 32 51 52 dID 170 270 34 25 2425 185 65 79 111 52 199 293 dVWRPY 125 208 112 102 20 47 1689 1156 49 49 77 42 leiden 12 13 14 15 16 17 group Base 0 28 24 3 17 13 Naive 542 0 0 1 0 0 Null 0 16 21 11 15 6 WT 0 24 30 8 30 1 d5 0 4 0 46 0 0 d8 0 5 1 12 2 1 dAD 0 9 15 13 6 0 dID 0 44 35 12 8 4 dVWRPY 0 16 12 15 12 0 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 \ group Base 1073 5 1307 5 762 25 7 556 14 28 179 163 Naive 0 0 1 0 0 0 0 0 0 0 0 0 Null 1844 35 750 0 1267 6 2 416 6 43 47 87 WT 156 44 126 2851 107 391 43 215 365 28 298 113 d5 14 2 33 1 17 13 7 33 9 764 22 4 d8 173 0 521 0 195 10 14 138 4 94 12 27 dAD 217 2956 126 2 214 106 4 506 30 30 55 61 dID 164 29 179 16 180 91 2426 215 48 47 214 287 dVWRPY 111 98 60 88 88 2149 25 226 667 47 77 39 leiden 12 13 14 15 16 group Base 0 28 25 3 17 Naive 542 0 0 1 0 Null 0 16 20 11 15 WT 0 25 32 8 28 d5 0 3 0 47 0 d8 0 6 1 13 1 dAD 0 9 16 13 6 dID 0 56 39 12 8 dVWRPY 0 16 13 15 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:10)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1465 16 991 3 25 919 9 373 28 189 105 0 30 Naive 0 0 0 0 0 0 0 1 0 0 0 542 0 Null 1143 2 1348 37 8 1581 4 213 39 90 35 0 16 WT 133 3187 179 47 434 159 55 145 31 113 251 0 25 d5 33 8 32 3 15 13 8 31 760 5 18 0 3 d8 569 3 213 2 8 157 14 91 91 33 6 0 7 dAD 156 10 336 3268 119 194 5 83 30 55 49 0 10 dID 183 51 288 29 77 177 2470 112 48 290 168 0 57 dVWRPY 64 270 151 111 2639 112 34 128 50 41 73 0 19 leiden 13 14 15 group Base 25 3 16 Naive 0 1 0 Null 23 11 15 WT 31 8 32 d5 0 39 1 d8 1 13 1 dAD 17 13 6 dID 39 12 10 dVWRPY 12 15 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1251 14 5 15 1175 743 14 665 29 198 0 30 26 Naive 1 0 0 0 0 0 0 0 0 0 542 0 0 Null 1097 0 39 4 965 1539 2 724 42 83 0 16 23 WT 302 3228 43 357 126 108 54 366 31 113 0 25 36 d5 57 6 1 14 23 12 8 28 767 6 0 3 0 d8 274 1 0 7 490 142 22 120 95 35 0 5 2 dAD 642 7 3026 87 129 161 6 156 33 58 0 10 17 dID 336 40 22 85 133 150 2480 312 48 286 0 56 37 dVWRPY 332 179 120 2630 54 71 35 161 50 41 0 19 13 leiden 13 14 15 group Base 3 18 11 Naive 1 0 0 Null 11 13 7 WT 8 33 0 d5 44 0 0 d8 13 2 1 dAD 13 6 0 dID 12 11 3 dVWRPY 15 11 0 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:11)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1550 1346 14 28 8 10 863 33 195 0 55 31 29 Naive 0 1 0 0 0 0 0 0 0 542 0 0 0 Null 2554 1206 2 6 30 4 523 43 91 0 28 17 27 WT 246 328 3345 328 49 53 90 33 104 0 157 24 36 d5 14 60 10 13 2 10 24 756 5 0 12 3 1 d8 282 278 3 10 1 10 454 107 33 0 8 6 2 dAD 287 829 9 125 2821 3 98 35 59 0 34 10 22 dID 313 369 50 90 24 2481 114 50 290 0 113 58 34 dVWRPY 147 386 329 2493 78 43 39 54 41 0 50 23 19 leiden 13 14 15 group Base 3 19 13 Naive 1 0 0 Null 11 16 7 WT 8 29 0 d5 59 0 0 d8 13 1 1 dAD 13 6 0 dID 11 10 4 dVWRPY 16 13 0 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1568 1379 13 25 11 15 894 27 183 0 26 6 31 Naive 0 0 0 0 0 0 1 0 0 542 0 0 0 Null 2458 1187 0 8 38 4 684 43 64 0 23 13 17 WT 368 309 3264 402 53 51 103 29 112 0 32 45 25 d5 32 54 6 14 0 9 28 770 5 0 1 3 3 d8 281 257 1 10 0 14 492 97 34 0 1 4 5 dAD 311 557 2 119 3083 6 111 34 56 0 21 22 10 dID 393 352 37 91 25 2529 132 49 284 0 40 17 41 dVWRPY 153 290 176 2715 98 35 50 52 43 0 21 50 19 leiden 13 14 group Base 3 16 Naive 1 0 Null 11 15 WT 8 29 d5 44 0 d8 12 1 dAD 13 6 dID 11 10 dVWRPY 16 13 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:12)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1488 1377 10 6 19 945 22 16 30 199 0 31 29 Naive 0 1 0 0 0 0 0 0 0 0 542 0 0 Null 2275 1238 0 38 3 792 5 3 44 89 0 17 24 WT 364 308 3124 47 52 103 219 342 31 110 0 23 29 d5 30 58 1 0 9 30 7 15 773 5 0 3 1 d8 264 279 0 0 22 472 5 9 98 37 0 6 2 dAD 271 624 4 3048 7 115 71 46 34 60 0 10 18 dID 374 357 30 24 2511 125 86 43 49 286 0 54 34 dVWRPY 141 264 137 88 34 45 1600 1231 51 42 0 19 14 leiden 13 14 15 group Base 6 2 17 Naive 0 1 0 Null 11 11 15 WT 41 8 29 d5 3 34 0 d8 2 12 1 dAD 24 13 6 dID 16 11 11 dVWRPY 38 14 13 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1329 1087 1426 4 5 13 34 29 30 157 0 32 28 Naive 0 0 1 0 0 0 0 0 0 0 542 0 0 Null 2301 1079 951 32 0 3 7 5 42 67 0 17 24 WT 259 298 136 46 2579 47 344 877 31 102 0 23 25 d5 24 59 32 0 0 8 9 15 773 4 0 4 1 d8 247 238 547 1 0 11 10 8 96 28 0 6 1 dAD 263 660 152 2958 0 3 115 46 32 55 0 10 21 dID 309 363 182 23 14 2503 92 74 51 277 0 55 33 dVWRPY 122 252 66 77 75 25 1883 1049 50 42 0 19 15 leiden 13 14 15 group Base 5 2 16 Naive 0 1 0 Null 10 11 16 WT 37 8 18 d5 3 37 0 d8 2 13 1 dAD 17 13 6 dID 14 11 10 dVWRPY 30 14 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1574 1377 10 10 30 2 901 21 30 160 0 31 27 Naive 0 0 0 0 0 0 1 0 0 0 542 0 0 Null 2502 1286 42 3 5 0 533 5 45 66 0 17 25 WT 354 278 47 46 1185 2338 98 252 31 92 0 23 23 d5 26 59 1 8 17 0 30 8 775 4 0 3 1 d8 276 282 1 14 9 0 483 5 92 26 0 5 1 dAD 276 563 3121 6 51 0 98 90 31 48 0 10 18 dID 374 356 34 2525 71 12 118 69 52 272 0 54 39 dVWRPY 138 241 85 32 1169 46 38 1796 52 37 0 19 15 leiden 13 14 15 group Base 6 2 16 Naive 0 1 0 Null 10 11 15 WT 38 8 17 d5 3 34 0 d8 2 12 1 dAD 20 13 6 dID 16 11 8 dVWRPY 37 14 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:04)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:05)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1286 1342 6 1181 4 12 32 28 31 195 0 30 27 Naive 0 0 0 1 0 0 0 0 0 0 542 0 0 Null 2167 1298 38 841 0 3 5 6 45 85 0 17 22 WT 284 309 50 109 2634 52 292 851 30 97 0 22 28 d5 21 58 1 32 0 10 7 16 779 4 0 3 1 d8 241 288 1 496 0 12 9 11 95 33 0 5 2 dAD 251 659 3010 123 1 5 86 55 31 58 0 10 22 dID 293 409 17 146 15 2499 82 84 50 285 0 55 36 dVWRPY 118 267 87 46 60 31 1774 1162 50 39 0 19 13 leiden 13 14 15 group Base 5 2 16 Naive 0 1 0 Null 11 11 16 WT 36 8 28 d5 3 34 0 d8 3 12 1 dAD 21 13 6 dID 18 11 11 dVWRPY 38 14 13 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:06)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:13)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1343 1262 5 11 2 30 887 23 352 28 177 0 32 Naive 0 0 0 0 0 0 1 0 0 0 0 542 0 Null 2400 1221 33 2 0 5 541 5 177 44 71 0 17 WT 168 233 43 46 2399 1031 88 288 339 30 94 0 23 d5 17 49 1 8 0 18 27 8 23 777 4 0 3 d8 254 270 0 14 0 10 466 6 42 96 31 0 5 dAD 232 792 2879 4 0 61 96 82 75 30 53 0 10 dID 204 310 37 2489 11 87 112 69 254 49 279 0 55 dVWRPY 103 242 75 31 55 1192 36 1745 102 57 36 0 19 leiden 13 14 15 group Base 27 2 16 Naive 0 1 0 Null 24 11 14 WT 22 8 18 d5 1 33 0 d8 2 12 1 dAD 18 13 6 dID 36 11 8 dVWRPY 12 14 12 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1515 19 916 4 582 20 15 766 26 178 78 0 31 Naive 0 0 0 0 0 0 0 1 0 0 0 542 0 Null 1546 2 1684 30 631 7 3 456 48 61 31 0 17 WT 145 3284 150 44 265 348 49 89 33 100 231 0 22 d5 19 8 13 1 47 12 9 26 773 5 19 0 3 d8 232 2 170 0 165 8 13 465 95 30 8 0 5 dAD 165 6 208 2920 689 104 4 92 31 51 34 0 10 dID 184 42 192 23 276 87 2485 124 49 296 139 0 54 dVWRPY 86 279 104 81 447 2433 35 49 54 39 61 0 19 leiden 13 14 15 group Base 27 2 18 Naive 0 1 0 Null 23 11 15 WT 33 8 29 d5 1 33 0 d8 3 12 1 dAD 18 13 6 dID 38 11 11 dVWRPY 17 14 13 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:10)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1349 1034 1465 3 4 16 18 24 28 174 0 30 28 Naive 0 0 1 0 0 0 0 0 0 0 542 0 0 Null 2363 1016 970 19 0 2 6 6 44 66 0 17 23 WT 362 264 130 39 2533 48 285 923 31 110 0 22 19 d5 28 57 30 0 0 8 9 13 769 5 0 3 1 d8 263 230 542 0 0 11 6 9 96 30 0 5 1 dAD 293 820 150 2809 0 2 101 26 31 51 0 10 22 dID 377 345 175 18 14 2500 66 70 47 281 0 48 37 dVWRPY 148 307 60 73 73 25 1882 987 46 40 0 19 14 leiden 13 14 15 group Base 3 6 15 Naive 1 0 0 Null 11 9 13 WT 8 30 26 d5 45 1 0 d8 13 2 1 dAD 13 17 6 dID 11 14 8 dVWRPY 16 28 13 computing neighbors
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:05)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:07)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:14)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1163 1139 1488 3 10 16 24 27 27 174 0 50 31 Naive 0 0 1 0 0 0 0 0 0 0 542 0 0 Null 1263 2125 939 25 0 2 8 6 44 64 0 25 17 WT 286 190 133 45 2803 42 306 638 33 109 0 161 22 d5 56 14 34 1 0 8 11 15 768 5 0 19 3 d8 269 213 544 0 0 13 8 10 93 33 0 7 5 dAD 825 241 148 2825 1 6 111 29 36 52 0 27 10 dID 368 244 169 17 20 2523 85 61 47 281 0 116 41 dVWRPY 301 106 59 71 96 26 2030 842 48 41 0 52 19 leiden 13 14 15 group Base 27 2 16 Naive 0 1 0 Null 21 11 15 WT 20 8 34 d5 1 34 0 d8 1 12 1 dAD 21 13 6 dID 20 11 8 dVWRPY 13 14 13
/scratch/local/20367146/ipykernel_1275877/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
InĀ [9]:
# End of Notebook
print("\nNotebook Ends")
Notebook Ends